6BWW | pdb_00006bww

Crystal structure of an acetate and Cymal-5 bound cytochrome P450 2B4 F429H mutant

PDB DOI: https://doi.org/10.2210/pdb6BWW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2017-12-15 Released: 2018-12-19
Deposition Author(s): Yang, Y.T., Waskell, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.206 (Depositor), 0.199 (DCC)
R-Value Work:
0.185 (Depositor), 0.179 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of cytochrome P450 2B4 with an acetate ligand and an active site hydrogen bond network similar to oxyferrous P450cam.

Yang, Y., Bu, W., Im, S., Meagher, J., Stuckey, J., Waskell, L.

(2018) J Inorg Biochem 185: 17-25

PubMed: 29730233 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jinorgbio.2018.04.015
Primary Citation Related Structures:
6BWW

Organizational Affiliation

Department of Anesthesiology, University of Michigan and VA Medical Research Center, 2215 Fuller Rd, Ann Arbor, MI 48105, USA.

Macromolecule Content

Total Structure Weight: 56.25 kDa
Atom Count: 4,183
Modeled Residue Count: 463
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2B4	A	472	Oryctolagus cuniculus	Mutation(s): 1 Gene Names: CYP2B4 EC: 1.14.14.1 Membrane Entity: Yes
UniProt
Find proteins for P00178 (Oryctolagus cuniculus) Explore P00178 Go to UniProtKB: P00178
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00178
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CM5 Query on CM5 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE C₂₃ H₄₂ O₁₁ RVTGFZGNOSKUDA-ZNGNCRBCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain N [auth A]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]